Molecular Modeling and Drug Discovery
- AutoDock: A molecular docking software that is free and open-source. It helps researchers predict the interaction between small molecules (e.g., drugs) and macromolecules (e.g., proteins). https://www.youtube.com/watch?v=k6tqCeDIwEk
- SwissDock: A free online molecular docking tool, which helps predict how small molecules (like drugs) interact with protein targets. It’s a great alternative for researchers working on molecular modeling without access to commercial software. https://www.youtube.com/watch?v=gztIfgMALuY
3D Modeling and Structural Biology
- PyMOL: An open-source molecular visualization system. It can help you visualize protein structures, analyze molecular interactions, and generate publication-quality figures without needing a commercial license. https://www.youtube.com/watch?v=h5wKppcyzOw
- Chimera: Another free tool for visualizing and analyzing molecular structures. It’s widely used for working with protein structures and their interactions. https://www.youtube.com/watch?v=OHJD8tzigGo
Genomics/Omics Analysis
- Galaxy: An open-source platform for data-intensive biomedical research. Galaxy allows users to create, run, and share analyses using pre-built tools in a user-friendly environment. https://www.youtube.com/watch?v=uVNdyrVDYYU
- Bioconductor: A collection of R packages for the analysis and comprehension of genomic data. It’s particularly useful in bioinformatics for analyzing data from high-throughput sequencing platforms. https://www.youtube.com/watch?v=FaeGsxJ32I]
Histology and Imaging Tools
- ImageJ/Fiji: A free and open-source software package for image processing and analysis, widely used in biomedical research. It’s ideal for analyzing histology images, fluorescence microscopy, and other types of microscopy data. Many plugins and user communities exist to extend its functionality for specific needs like quantifying immunohistochemical staining or cell segmentation. https://www.youtube.com/watch?v=y567dfZ_reI
- QuPath: A free, open-source software for digital pathology and bioimage analysis. It’s designed to assist with analyzing histopathological images, including tissue segmentation, object detection, and quantification of features like cell counts and staining intensities. https://www.youtube.com/watch?v=mvZlU_fI75o
Microscopy and High Content Imaging
- CellProfiler: A free, open-source software for high-throughput image analysis. It can be used to analyze microscope images and quantify cellular features, making it an effective tool for histology image analysis. https://www.youtube.com/playlist?list=PLXSm9cHbSZBBy7JkChB32_e3lURUcT3RL
- Ilastik use machine learning and deep learning algorithms to analyze complex image datasets. They can assist in tasks like segmentation, classification, and object detection in microscopy images. They are particularly useful when dealing with large-scale datasets or complex imaging, such as analyzing high-content screens. https://www.youtube.com/playlist?list=PLeM_d8ZXiMCNXtVFvwAW23yXfTDsGFk5t
Gene Function and Network Analysis
- Cytoscape is widely used for creating and visualizing biological networks, particularly protein-protein interaction networks, gene regulatory networks, and other types of molecular interactions. It allows users to import data, build networks, and visualize how various biological entities (e.g., proteins, genes) are connected. https://www.youtube.com/playlist?list=PLKuX62ahaHyJ2ZgSKYNusvLbrhvW6KdWz
- GeneMANIA is an online tool for gene function prediction based on network analysis and gene-gene interactions. It’s especially useful for identifying genetic interactions and understanding the roles of specific genes in diseases. https://www.youtube.com/watch?v=WqX3waaSyYc
Miscellaneous tools/Data Sharing and Protocols:
- Protocols.io: A platform for sharing research protocols. It’s an excellent resource for finding cost-effective methods and experimental designs that others have used in their research, potentially saving you time and resources. https://www.youtube.com/watch?v=XvbMnPG6ckQ
- Cytobank (Beckman Coulter) is an online platform for flow cytometry data analysis, including single-cell analysis and multi-parameter data visualization. It’s highly useful for members working with single-cell omics and immunology. https://www.youtube.com/watch?v=tZNVdAZSTdE